I would just uninstall it with Add/Remove programs after copying the backup stuff, and then check the various install locations listed below for leftover folders and files. Run CCleaner "Issues" or any other Reg Cleaner you may use afterwards (make a backup), and you should be good to go.
First I would check to make sure you have the Opera 10 File and Folder structure after your install into the Opera 9 folder, as it differs from Opera 9.

C:\Documents and Settings\<username>\Local Settings\Application Data\Opera
Copy "Thumbnails" and "Icons" folders, which are your custom "Speed Dial Images" and "Favicons", and the "Mail" folder if you use Opera Mail.
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C:\Documents and Settings\<username>\Application Data\Opera\Opera
Copy the entire folder, which is only about 1.5mb. (EDIT: In my case)
From here you can copy back into the new install, things such as:
"bookmarks.adr", "notes.adr", "toolbar folder" if you have modified toolbars, "wand.dat" if you use the wand for log-ins, "speeddial.ini" if you have custom speeddials.
Your custom "Skins" may be here or in the Program Files folder. I place all mine in Program files, but I'm not sure which is the default.
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C:\Program Files\Opera
From here I backup the "UI", "Skins", and "Styles" folders.
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In the folder you keep these backups, I would place the various files and folders in subfolders with their respective names. "Application Data", Local Settings", and "Program Files".
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That I think will cover any personalisations you made to Opera, and will give you a means of recovering just about everything in the event of any future problems.
One other thing I do is make an "HTML" backup of bookmarks, which you can make from within the opened browser, "File\Import and Export\Export Bookmarks As HTML". This file can usually be imported easily into other browsers.
This seems a lot to do, and some of the above would possibly be OK to leave, but to be sure of getting rid of the all the stuff tied to Opera 9, it's worth the effort, and it gives you a backup which you can update from time to time.
It was the only way I could find to completely get rid of my Opera 10 Beta install without having to start again setting up all my personalizations, and I have a lot.
Hope that helps.